I can't edit it from StackController.app though..
I kind of follow the manual installation, but it's more complicated.
These steps should work:
Copy StackController.app to your /Applications directory.
Copy Stacks.app from within the StacksController.app directory to /Applications.
Set permissions to 755 on both executables.
Copy the com .plist to /System/Library/LaunchDaemons.
Reboot.
You should have a blank Stacks icon on your SpringBoard, along with the stack in the corner.
Open up a shell session and run ps -ax, then kill -9 the stackbinary process.
Quickly move your fourth dock icon out and move the blank Stacks icon into the fourth spot, then wait for Stacks to respawn and you should be good.

It's partially working, at best.
You can't configure the icons, for some reason, or the shape of the stack.
Also, you can't install or remove it, since the information in N45AP.plist doesn't determine if icons show or not anymore..
We should work to mod this.